I am trying to access our internal intranet and sharepoint sites from our blackberry handsets, when accessing the sites i am prompted with authentication prompt requesting a username, domain and password.
I can access the sites after manually authenticating.

Is there anyway of accessing the sites without the authentication prompt appearing (pass through)? I have trawled the forums and cannot find a way.

BES 5.0 SP2 adds integrated windows authentication support for kerberos only. SP does support kerberos with additional setup, but out of the box it uses NTLM authentication. Your intranet may only use NTLM too so you would bump into the same issue being prompted for credentials every new session.

In 4.1, the best you can do is pre-populate the domain field or work some proxy magic and have all users funnel to SharePoint/intranet through a single user account.

There are other alternatives for SharePoint that will work with 4.1 and above. We build an application called SilverDust that allows you to connect and edit to your SharePoint content (lists, document libraries, calendars), which only requires you to sign on once to reach the content. Check out my signature for a link to more information.